For ChIP, double cross-linking with Di(N-succinimidyl)-glutarate and formaldehyde was used as described (Nowak et al., 2005). After sonication, lysates were incubated with the corresponding antibodies, histones-DNA complexes were immunoprecipitated with dynabeads and DNA was purified using columns. Libraries were prepared following the standard illumina Pair-end protocol. Libraries were prepared following the standard illumina Pair-end protocol.